https://github.com/cran/spatstat
Revision 967fc2de73b44e75d7d8497a8d21770604051e17 authored by Adrian Baddeley on 21 December 2011, 08:53:46 UTC, committed by cran-robot on 21 December 2011, 08:53:46 UTC
1 parent 266eff5
Tip revision: 967fc2de73b44e75d7d8497a8d21770604051e17 authored by Adrian Baddeley on 21 December 2011, 08:53:46 UTC
version 1.25-1
version 1.25-1
Tip revision: 967fc2d
Jest.R
# Jest.S
#
# Usual invocation to compute J function
# if F and G are not required
#
# $Revision: 4.18 $ $Date: 2011/04/19 02:14:27 $
#
#
#
"Jest" <-
function(X, ..., eps=NULL, r=NULL, breaks=NULL, correction=NULL) {
X <- as.ppp(X)
W<- X$window
rmaxdefault <- rmax.rule("J", W)
brks <- handle.r.b.args(r, breaks, W, rmaxdefault=rmaxdefault)$val
# compute F and G
FF <- Fest(X, eps, breaks=brks, correction=correction)
G <- Gest(X, breaks=brks, correction=correction)
# initialise fv object
rvals <- FF$r
rmax <- max(rvals)
Fvals <- FF[[attr(FF, "valu")]]
Z <- fv(data.frame(r=rvals, theo=1),
"r", substitute(J(r), NULL),
"theo",
. ~ r,
c(0,rmax),
c("r", "%s[pois](r)"),
c("distance argument r", "theoretical Poisson %s"),
fname="J")
# compute J function estimates
# this has to be done manually because of the mismatch between names
ratio <- function(a, b) {
result <- a/b
result[ b == 0 ] <- NA
result
}
Fnames <- names(FF)
Gnames <- names(G)
if("raw" %in% Gnames && "raw" %in% Fnames) {
Jun <- ratio(1-G$raw, 1-FF$raw)
Z <- bind.fv(Z, data.frame(un=Jun), "hat(%s)[un](r)",
"uncorrected estimate of %s", "un")
attr(Z, "alim") <- range(rvals[FF$raw <= 0.9])
}
if("rs" %in% Gnames && "rs" %in% Fnames) {
Jrs <- ratio(1-G$rs, 1-FF$rs)
Z <- bind.fv(Z, data.frame(rs=Jrs), "hat(%s)[rs](r)",
"border corrected estimate of %s", "rs")
attr(Z, "alim") <- range(rvals[FF$rs <= 0.9])
}
if("han" %in% Gnames && "cs" %in% Fnames) {
Jhan <- ratio(1-G$han, 1-FF$cs)
Z <- bind.fv(Z, data.frame(han=Jhan), "hat(%s)[han](r)",
"Hanisch-style estimate of %s", "han")
attr(Z, "alim") <- range(rvals[FF$cs <= 0.9])
}
if("km" %in% Gnames && "km" %in% Fnames) {
Jkm <- ratio(1-G$km, 1-FF$km)
Z <- bind.fv(Z, data.frame(km=Jkm), "hat(%s)[km](r)",
"Kaplan-Meier estimate of %s", "km")
attr(Z, "alim") <- range(rvals[FF$km <= 0.9])
}
if("hazard" %in% Gnames && "hazard" %in% Fnames) {
Jhaz <- G$hazard - FF$hazard
Z <- bind.fv(Z, data.frame(hazard=Jhaz), "hazard(r)",
"Kaplan-Meier estimate of derivative of log(%s)")
}
# set default plotting values and order
nama <- names(Z)
fvnames(Z, ".") <- rev(nama[!(nama %in% c("r", "hazard"))])
# add more info
attr(Z, "F") <- FF
attr(Z, "G") <- G
unitname(Z) <- unitname(X)
return(Z)
}
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